Coexpression cluster:C1818

Full id: C1818_brain_temporal_occipital_diencephalon_cerebellum_olfactory_cerebral

Phase1 CAGE Peaks

Hg19::chr19:36367501..36367512,-	p@chr19:36367501..36367512 -
Hg19::chr19:42470973..42470984,+	p4@CU679344
Hg19::chr2:131769317..131769328,+	p13@ARHGEF4
Hg19::chr9:120173722..120173724,-	p@chr9:120173722..120173724 -
Hg19::chr9:34523008..34523018,-	p5@ENHO

Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

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No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

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GO ID	GO name	FDR corrected p-value
GO:0019904	protein domain specific binding	0.0265630519251148
GO:0005089	Rho guanyl-nucleotide exchange factor activity	0.0265630519251148
GO:0035023	regulation of Rho protein signal transduction	0.0265630519251148
GO:0005088	Ras guanyl-nucleotide exchange factor activity	0.0265630519251148
GO:0007266	Rho protein signal transduction	0.0265630519251148
GO:0005085	guanyl-nucleotide exchange factor activity	0.0334864005651713
GO:0046578	regulation of Ras protein signal transduction	0.0334864005651713
GO:0007265	Ras protein signal transduction	0.0334864005651713
GO:0005083	small GTPase regulator activity	0.0334864005651713
GO:0051056	regulation of small GTPase mediated signal transduction	0.0334864005651713
GO:0030695	GTPase regulator activity	0.0449568093510163
GO:0009966	regulation of signal transduction	0.0470976097963028
GO:0007264	small GTPase mediated signal transduction	0.0474961280330408

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
central nervous system	5.73e-72	81
neural tube	3.20e-71	56
neural rod	3.20e-71	56
future spinal cord	3.20e-71	56
neural keel	3.20e-71	56
regional part of nervous system	7.33e-66	53
regional part of brain	7.33e-66	53
brain	8.42e-65	68
future brain	8.42e-65	68
nervous system	4.05e-64	89
telencephalon	7.65e-61	34
brain grey matter	2.26e-60	34
gray matter	2.26e-60	34
regional part of forebrain	2.78e-59	41
forebrain	2.78e-59	41
anterior neural tube	2.78e-59	41
future forebrain	2.78e-59	41
regional part of cerebral cortex	8.96e-58	22
cerebral hemisphere	1.17e-53	32
regional part of telencephalon	1.35e-53	32
neural plate	6.11e-53	82
presumptive neural plate	6.11e-53	82
cerebral cortex	1.34e-50	25
pallium	1.34e-50	25
neocortex	3.65e-50	20
neurectoderm	3.75e-50	86
pre-chordal neural plate	8.66e-45	61
ecto-epithelium	6.41e-43	104
ectoderm-derived structure	1.06e-33	171
ectoderm	1.06e-33	171
presumptive ectoderm	1.06e-33	171
structure with developmental contribution from neural crest	2.47e-32	132
adult organism	7.28e-32	114
organ system subdivision	5.67e-24	223
gyrus	1.59e-18	6
tube	8.03e-16	192
temporal lobe	2.30e-15	6
parietal lobe	9.86e-15	5
occipital lobe	1.78e-14	5
limbic system	8.05e-14	5
posterior neural tube	3.29e-13	15
chordal neural plate	3.29e-13	15
pons	4.44e-13	3
anatomical cluster	8.22e-12	373
neural nucleus	1.43e-11	9
nucleus of brain	1.43e-11	9
brainstem	2.10e-11	6
anatomical conduit	3.17e-11	240
organ part	6.97e-11	218
middle temporal gyrus	1.05e-09	2
Ammon's horn	1.36e-09	2
lobe parts of cerebral cortex	1.36e-09	2
hippocampal formation	1.36e-09	2
limbic lobe	1.36e-09	2
epithelium	1.56e-09	306
cell layer	2.29e-09	309
locus ceruleus	3.81e-09	2
brainstem nucleus	3.81e-09	2
hindbrain nucleus	3.81e-09	2
segmental subdivision of hindbrain	9.44e-09	12
hindbrain	9.44e-09	12
presumptive hindbrain	9.44e-09	12
segmental subdivision of nervous system	4.69e-08	13
regional part of metencephalon	8.68e-08	9
metencephalon	8.68e-08	9
future metencephalon	8.68e-08	9
basal ganglion	1.02e-07	9
nuclear complex of neuraxis	1.02e-07	9
aggregate regional part of brain	1.02e-07	9
collection of basal ganglia	1.02e-07	9
cerebral subcortex	1.02e-07	9
multi-tissue structure	5.10e-07	342
frontal cortex	7.80e-07	3
spinal cord	9.02e-07	3
dorsal region element	9.02e-07	3
dorsum	9.02e-07	3

Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
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ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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This analysis result is provided for C0 - C305 clusters.